S4methods: S4 Generics & Methods for Package 'FAiR'

In FAiR: Factor Analysis in R

Description

It is not necessary to understand this help page if one merely wants to estimate a factor analysis model. This help page is intended for those who want to modify or extend FAiR or otherwise want some idea of how FAiR works “behind the scenes”.

Factanal is just a wrapper around a call to genoud in the rgenoud package. These S4 generic functions are passed to various arguments of genoud as part of the optimization process. With the exception of the methods for create_start, it would be very unusual for any of these methods to be called directly by the user.

Usage

## S4 method for signature 'restrictions,manifest.basic'
fitS4(par, restrictions, manifest, lower, mapping_rule)
## S4 method for signature 'restrictions,manifest.basic'
bfgs_fitS4(par, restrictions, manifest, helper, lower)
## S4 method for signature 'restrictions,manifest.basic'
gr_fitS4(par, restrictions, manifest, helper, lower)
## S4 method for signature 'restrictions,manifest.basic'
bfgs_helpS4(initial, restrictions, manifest, done, lower)
## S4 method for signature 'restrictions,manifest.basic'
create_start(number, start, restrictions, manifest, reject)

Arguments

par	A numeric vector containing values for all the free parameters to be estimated, which corresponds to the par argument for genoud and for optim.
initial	Same as par.
restrictions	An object of restrictions-class.
manifest	An object of manifest-class.
lower	A small numeric scalar indicating the lower bound for positive definiteness or minimum uniqueness; see the corresponding argument to Factanal.
mapping\_rule	a logical indicating whether to invoke the mapping rule in semi-exploratory models. It takes the value of FALSE when called by optim.
helper	A list that contains necessary information for the bfgs_fitS4 and gr_fitS4 methods that is passed to the BFGShelp argument for genoud.
done	A logical indicating whether the optimization has terminated or could terminate immediately if a stopping condition is met; see the documentation of the BFGShelp argument to genoud.
number	An integer representing the number of starting values to create
start	A numeric vector or matrix containing initial communality estimates
reject	Logical indicating whether to reject starting values that fail the constraints required by the model
...	Further arguments to be passed to downstream functions; not currently used.

Details

The fitS4 method is responsible for producing a complete numeric vector of fit criteria and is passed to the fn argument of genoud. The default method simply calls restrictions2model and then calls an internal function that evaluates all the functions in the criteria slot of the object of restrictions-class.

The bfgs_fitS4 method produces a scalar fit criterion, and this method is passed to the BFGSfn argument of genoud and is in turned passed to the fn argument of optim. Usually, this criterion is the last criterion produced by the fitS4 method, which is the discrepancy function. The gr_fitS4 method produces the gradient of the function defined by the bfgs_fitS4 method under traditional maximum likelihood estimation; otherwise it is an internal function. Either way, this function is passed to the gr argument of genoud and optim. Both bfgs_fitS4 and gr_fitS4 take an argument called helper, which is produced by the bfgs_helpS4 method and corresponds to the BFGShelp argument of genoud. The BFGShelp method produces a list that contains information about the initial value of the genetic individual when optim is called. The bfgs_fitS4 methods and gr_fitS4 methods can behave differently depending on the contents of helper.

The create_start method creates a matrix of starting values that is then passed to the starting.values argument of genoud. If you think the starting values are inadequate in a particular situation, it is much easier to create a matrix of starting values in the global environment and pass it through the ... of Factanal to the starting.values argument of genoud yourself. See Factanal for details on doing so.

Value

fitS4	produces a numeric vector of fits
bfgs_fitS4	produces a numeric scalar as a fit
gr_fitS4	produces a numeric vector that is the gradient at the scalar fit
bfgs_helpS4	produces a list of ancillary material for bfgs_fitS4 and gr_fitS4
create_start	produces a numeric matrix that constitutes the starting population

Methods

There are methods for every flavor of restrictions-class, although in many cases the methods are simply inherited. Currently, there are only methods for objects of class "manifest.basic", which are inherited by objects of class "manifest.data" and "manifest.data.mcd". However, it is possible to tailor methods for different flavors of manifest-class or to create new classes that inherit from restrictions-class and write (some) methods for them.

Author(s)

Ben Goodrich

See Also

Factanal, manifest-class, restrictions-class and genoud

Examples

  showMethods("fitS4")
  showMethods("bfgs_fitS4")
  showMethods("gr_fitS4")
  showMethods("bfgs_helpS4")
  showMethods("create_start")

FAiR documentation built on May 29, 2017, 6:08 p.m.